Professor Terence Stephenson: ‘I don’t think it’s possible in quite a small country of 60 million people to have 200 to 300 24/7 acute centres offering every single discipline.’ Photograph: Graham Turner for the Guardian

The vicissitudes of medical politics mean being de facto leader of the UK's 200,000 doctors is never easy. But Professor Terence Stephenson's in-tray as he takes over on Wednesday as chair of the Academy of Medical Royal Colleges (AoMRC) is even more daunting than usual.

England's NHS is struggling to deliver an arguably impossible £20bn NHS efficiency drive, and there is continuing frostiness between many parts of the medical establishment and the health secretary, Andrew Lansley, over the failure of their revolt against the health and social care bill.

Stephenson's manifesto for the academy post listed an array of other challenges facing the NHS and the medical profession, including service reconfiguration, failing hospitals, public health and obesity. His trenchant but thoughtful views on the last, such as backing for Danish-style fat taxes, earned him an invitation to dinner with celebrity chef and healthy eating campaigner Jamie Oliver to brainstorm potential solutions.

But it is the growing pressure to radically rethink how NHS care is delivered, especially the role of hospitals, that demonstrates Stephenson's willingness to acknowledge a problem and talk in considered but necessarily bold terms about fixing it.

The academy represents the views of its 20 member royal colleges and faculties of medicine, but does not determine their policies. So before delivering his assessment of NHS care, Stephenson is careful to stress: "What I'm expressing today are personal views." His verdict: "It's a bit like a school report – satisfactory but could do better. You can take the view that [the failings at] Mid Staffs [NHS trust] is just an isolated case, but it would be naive to think some of those issues don't pervade."

Given the big increase in funding of the NHS since 2000, it is unacceptable that outcomes for patients in many areas of care still lag behind other big European countries, he says. So if lack of investment isn't the reason, what is? "We do try to deliver care too broadly across too many centres," he replies. "We're trying for that aphorism that everybody wants open heart surgery in a cottage hospital. It's just not deliverable."

The problem, he elaborates, is that "we broadly have an NHS structure that's not much different from 1948. Most of the hospitals that were brought into the NHS in 1948 are still there, and we've got to grasp that. I don't think it's possible in quite a small country of 60 million people to have 200 to 300 24/7 acute centres offering every single discipline."

He describes the duplication arising from so many hospitals – often not far from one another – offering the same services as "wasteful".

Stephenson's vision of the NHS's future is of greater centralisation of acute medical services. Drawing on his knowledge of children's health – he was president of the Royal College of Paediatrics and Child Health (RCPCH) until May – he says: "Modelling we did on paediatrics [showed that] we're running 220 24/7 centres across [the UK's] four countries and we thought it should come down to 170. Broadly, we need to move to a smaller number of bigger centres giving treatment that's either hi‑tech, risky or rare."

Greater concentrations of staff handling greater numbers of acute cases will improve their skills and so benefit patients, he believes. Many other medical leaders, such as the NHS Confederation and the King's Fund share his analysis, as do the NHS chief executive, Sir David Nicholson, and the health select committee chairman, Stephen Dorrell.

Stephenson acknowledges that local campaigns against the potential loss of an A&E, maternity or any other unit are inevitable. But he points to the reorganisation of childbirth services in Manchester, and the clinical benefits that have flowed from the centralisation of stroke and trauma care in London as proof that the NHS can overcome opposition and do the right thing for patients. While hospitals would lose certain inpatient services, some would still look after those less seriously unwell, and so parts of hospitals need not all necessarily fall into disuse, he explains.

"We're not suggesting local populations have no access to medical care," he says, by way of reassurance; just that sicker patients may in future have to travel farther.

While politicians have to play their part in persuading the public about why such changes are necessary, doctors are best placed to do that, he suggests, citing their key role in the recent, contentious NHS "safe and sustainable" review of children's heart surgery provision in England, which will see four of the 11 existing units close.

Stephenson, 54, a paediatrician, is incisive and articulate. As the RCPCH president he was centrally involved in the medical community's (failed) efforts to thwart the health and social care bill, though as a member of the NHS Future Forum he also tried to improve the plans, which many royal colleges and health unions, including the British Medical Association, wanted abandoned altogether. He dodges a question about the state of relations now between medics and ministers, saying simply: "The act is now the act and my personal view is there's no point in looking backwards."

One result of the "NHS Arab spring" is that the Department of Health wants to deal as far as possible with the academy as the voice of the medical profession rather than a plethora of disparate groups of doctors. That will make Stephenson a key player in the new NHS. The academy has already been talking to the health service's national commissioning board about what standards of care should be in an era when there are general concerns that clinical commissioning groups, which will replace primary care trusts in 2013, could lead to an even greater postcode lottery in healthcare.

Stephenson says if the government in London, Edinburgh, Cardiff or Belfast seeks the academy's views, "there's a compact that goes with that. If they come to us for advice and we give it, and they act on that advice, we can hardly be pouring criticism on them. [But] if they come to us for advice and ignore it, and it goes wrong, we would be entitled to pass independent comment."

It sounds as though this comment is aimed equally at outspoken, anti-bill members of his own profession as at the famously non-listening Lansley.

As Stephenson says, with so many big issues pressing on the NHS – the ageing population, the slowly exploding obesity timebomb, and the need to fund new drugs – it is a time for leadership, tough decisions and long-term thinking, and doing the right thing for patients.